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We are using some custom made and predefined Haloplex kits. I was wandering how the best practice for variant detection should be "adapted". One of the biggest challenges we are facing is that we can not do a VQSR due to the low number of variants detected. So we have to use an hard filtering step, but here again the nature of the reads, all produced by enzyme restrictions, make some filters inappropriate like the ReadPosRankSumTest as the reads are not randomly produced.
I was wondering if the community has any experience with this kind of data and how the hard filtering should be made?
Thanks for your help.